Conserved quantities and total derivatives?

It seems to me that you are confusing a generic notion of total derivative and the so called Lagrangian derivative (also known as material derivative).

Let us start from scratch. In Cartesian coordinates, a fluid or a generic continuous body is first of all described by a class of differentiable (smooth) maps from $\mathbb R^3$ to $\mathbb R^3$: $$x=x(t,y)\:, \quad x \in \mathbb R^3\:.$$ For every $t\in \mathbb R$, the map $\mathbb R^3 \ni y \mapsto x(t,y) \in \mathbb R^3$ associates the particle with initial position $y$ with the position $x$ of the same particle at time $t$.

For every fixed $t$, the map above is supposed to be inverible with differentiable (smooth) inverse, and the two maps $\mathbb R^3 \ni y \mapsto x(t,y) \in \mathbb R^3$ and $\mathbb R^3 \ni x \mapsto y(t,x) \in \mathbb R^3$ are jointly smooth in all variables simultaneously.

At time $t$, the velocity of the particle with initial position $y$ is consequently given by: $$v_L(t,y) = \frac{\partial x}{\partial t}\:.$$ The formula above pictures the field of velocities in the so called Lagrangian description: physically relevant quantities, at a given value of time, are viewed as functions of the initial position of the particles forming the continuous body. It is however often more convenient to describe this velocity as a function of the position in space at time $t$. We obtain this way the so called Eulerian description of the field of velocities: $$v(t,x) := v_L(t,y(t,x))\:.$$ (I will not make use on an index $E$, henceforth assuming that what it is not Lagrangian is automatically Eulerian.) $x$ is a given point in space at time $t$. At that time it is crossed by the particle with initial position $y(t,x)$.

Generally speaking, if $S$ is a (Cartesian) tensor field defined on the continuous body, we have two representations. The Lagrangian one $S_L(t,y)$ and the Eulerian one $S(t,x)$, where, obviously, $$S(t,x) = S_L(t,y(t,x))\quad \mbox{and}\quad S_L(t,y)= S(t,x(t,y))\:.$$ It is sometime convenient to compute the derivative of $S$ along the stories of the particles of continuous body while representing the obtained tensor field in Eulerian picture.

For instance, the acceleration field is $$a(t,x)= \left.\frac{\partial }{\partial t} v_L(t,y)\right|_{y=y(t,x)}\:.$$ Notice that the time derivative is correctly computed in Lagrangian representation, since we have to follow each particle separately. The RHS of the identity above reads, only exploiting Eulerian objects: $$a(t,x) = \frac{\partial v}{\partial t} + v \cdot \nabla_x v(t,x)\:.$$ (It is an easy exercise to establish that identity from definitions.)

In general the Lagrangian derivative of a tensor field (represented in Eulerian picture) $S(t,x)$ is defined as: $$\frac{DS}{Dt} := \frac{\partial S}{\partial t} + v(t,x)\cdot \nabla_x S(t,x)\qquad(1)$$ It turs out that: $$\left.\frac{DS}{Dt}(t,x)\right|_{x=x(t,y)}= \frac{\partial}{\partial t} S_L(t,y)\:,\qquad (2)$$ so that, the Lagrangian derivative is just a way to compute time derivatives along the stories of the particles of the continuous body remaining in Eulerian representation.

Remark. This Lagrangian derivative is the one you call total derivative, but its physical meaning is very precise as I illustrated above. In the rest of this post I keep denoting it by $D/Dt$ instead of $d/dt$.

Let us come to the conservation law of the mass. First of all, we have to endow our continuous system with a density of mass $\rho$. As before, we can adopt either an Eulerian or Lagrangian description: $$\rho= \rho(t,x)\qquad \mbox{and}\quad \rho_L= \rho_L(t,y):= \rho(t,y(t,x))\:.$$ The most clear statement concerning conservation of mass is the following.

For every (sufficiently regular) portion $V_L$ of the initial configuration of continuous body, corresponding to a portion $V_t$ at each value $t$ of time, $$V_t = \{x \in \mathbb R^3 \:|\: x = x(t,y)\:, y \in V_L\}\:,$$ the mass included in $V_t$ does not change in time: $$\frac{d}{dt} \int_{V_t} \rho(t,x) dx =0\:,\qquad(3)$$

Let us transform this requirement into the equivalent local statement. Passing to the Lagrangian picture, (1) reads: $$\frac{d}{dt} \int_{V_L} \rho(t,x(t,y)) |J_t| dy =0$$ that is $$\frac{d}{dt} \int_{V_L} \rho_L(t,y) |J_t| dy =0$$ where $J_t$ is the determinant of the Jacobian matrix of elements $\frac{\partial x_i}{\partial y_j}$. Since in (2) $V_L$ does not depend on time and everything is regular (the integrand is smooth and $V_L$ can always be assumed to be bounded) we can swap the symbol of derivative and that of integral (essentially taking advantage of Lebesgue's dominated convergence theorem): $$ \int_{V_L} \left(\frac{\partial}{\partial t}\rho_L(t,y)\right) |J_t| + \rho_L(t,y) \frac{\partial}{\partial t} |J_t| dy =0\:.$$ It is possible to prove (it is not so simple actually), that $\frac{\partial}{\partial t} |J_t| = |J_t|\nabla_x \cdot v(t,x)|_{x=x(t,y)}$. Using it in the LHS of the found identity and taking (1) and (2), into account, we find that (3) implies (in fact is equivalent to): $$ \int_{V_L} \left( \left.\frac{D\rho}{Dt}\right|_{x=x(t,y)}+\rho_L(t,y) \left.\nabla_x \cdot v(t,x)\right|_{x=x(t,y)}\right) |J_t| dy =0\:.\qquad (4)$$ In other words, coming back to Eulerian variables: $$ \int_{V_t} \frac{D\rho}{Dt}+\rho(t,x) \nabla_x \cdot v(t,x) dx =0\:.\qquad(5)$$ Form (4) or (5), using the fact that the integrand is continuous and $V_L$ or $V_t$ substantially are arbitrary, ones infers that the integral version of the law of mass conservation (3) is equivalent to the local requirement in Eulerian formulation: $$\frac{D\rho}{Dt}+\rho(t,x) \nabla_x \cdot v(t,x) = 0 \qquad (6)\:.$$ Finally, makig use of the definition of Lagrangian derivative (1), that identity can equivalently be stated as: $$\frac{\partial\rho}{\partial t}+ \nabla_x \cdot \rho(t,x) v(t,x) = 0 \qquad (7)\:.$$

Remark. A continuous body is incompressible if the volume measure $V_t$ of its portions $V_L$ remains constant along its story: $$\frac{d}{dt} \int_{V_t} dx =0\:.\qquad(3)'$$ Dealing with as before, one immediately sees that it is completely equivalent to say that (it would be enough to everywhere replace $\rho$ for $1$) $$\nabla_x \cdot v(t,x) = 0 \qquad (6)'\:.$$ Consequently, the law of conservation of mass for an incompressible continuous body, from (6),symply reads: $$\frac{D\rho}{Dt}=0\:. \qquad (8)$$ This is the equation you pointed out in the case of the law of conservation of mass. However, with that interpretation, it holds for incompressible bodies only, the general formulation being (6)'.

For a generic quantity $\rho$ (even vectorial or tensorial), (8) simply says that the quantity is constant in time along the story of every particle of the system, though that constant may depend on the particle.

For the sake of completeness, let me say a few words about another popular formulation of the conservation mass law. Starting from (7), integrating both sides in a geometric volume $U$ (so, not a portion of continuous body, but a geometric volume at rest with the reference frame we are using), we have: $$\int_U \frac{\partial \rho}{\partial t} dx = - \int_U \nabla_x \cdot \rho v(t,x) dx\:.$$ Thus, divergence theorem leads to the most popular version of the considered law whose meaning is illustrated in other answers to your question, so I will not spend any word on it: $$\frac{d}{dt}\int_U \rho(t,x) dx = - \int_{+\partial U} \rho v(t,x)\cdot n dS(x)\:,\qquad (9)$$ where $n$ is the outward unit vector at $x\in \partial U$.

As a final remark regarding the theory of continuous bodies, let me stress that the notion of Lagrangian derivative plays a crucial role in developing the theory of continuous bodies. For instance "$F=ma$" has to be written, for every portion $V_L$ of continuous body, exploiting the Lagrangian derivative: $$\frac{d}{dt}\int_{V_t} \rho(t,x) v(t,x) dx = F_{V_t}$$
that is, with some elementary manipulations, taking (6) into account, $$\int_{V_t} \rho(t,x) \frac{Dv}{Dt}(t,x) dx = F_{V_t}\:.$$

Remark. Dealing with Hamiltonian mechanics, there is a similar conservation law concerning probability when one studies statistical ensembles, i.e. statistical (Hamiltonian) mechanics. In that situation, in fact, Liouville's theorem establishes that the Hamiltonian evolution preserves the canonical volume of the space of phases. In other words (6)' holds true, where $v$ is the field of Hamiltonian velocities $(dq/dt,dp/dq)$. As a consequence the law of conservation of probabilities, described by the Liouville density $\rho$, can be stated in the simpler version: $$\frac{D\rho}{Dt}=0\:,$$ which, in turn, adopting the standard notation of statistical Hamiltonian mechanics, reads: $$\frac{d\rho}{dt}=0\:,$$ and, eventually, can be re-formulated into the celebrated Liouville equation form: $$\frac{\partial \rho}{\partial t} + \{\rho , H\}=0\:.$$

The Basic Idea

Physically the total derivative tells you how a quantity changes when it is subjected to a space and time dependent velocity field. In physics we usually call it the material derivative.

An Intuitive Example

Suppose $\rho(\mathbb{x},t)$ measures the temperature of a fluid, according to a thermometer immersed at the point $\mathbb{x}$ and time $t$. Now suppose the thermometer moves through the fluid, with position vector $\mathbb{x}(t)$.

After a small time $dt$ there is a corresponding change in position $d\mathbb{x}$. The temperature change observed on the thermometer will be

$$d\rho = \frac{\partial \rho}{\partial t}dt + \frac{\partial \rho}{\partial\mathbb{x}}\cdot d\mathbb{x}$$

Morally this approximates the total change as the instantaneous rate of change in each spacetime direction, multiplied by the corresponding change in spacetime.

Now dividing through by $dt$ (which can be made mathematically rigorous) you obtain the usual formula

$$\frac{d\rho}{dt} = \frac{\partial\rho}{\partial t}+\frac{\partial \rho}{\partial\mathbb{x}}\cdot \frac{d\mathbb{x}}{dt}=\frac{\partial\rho}{\partial t}+\nabla\rho\cdot\mathbb{u}$$

Conserved Quantities

We say that $\rho$ is conserved (or constant) along the flow of the fluid if

$$\frac{d\rho}{dt}=0$$

Integrating up we find that

$$\rho(\mathbb{x}(t),t) = \rho(\mathbb{x}(t_0),t_0)$$

As Joce noted in his comment, different paths $\mathbb{x}(t)$ may still have different values for $\rho$. The conservation condition only says that $\rho$ is constant along each path.

You are right to think this isn't very interesting at present. But it's a useful notion when coupled with other physical conservation laws.

A Physical Application

One of these is the conservation of mass. It's easy to derive this and see where the total derivative comes in. Take $\rho(\mathbb{x},t)$ to be the density of the fluid. Then the total mass of fluid in a volume $V$ is

$$M = \int_V \rho\ dV$$

Every second, mass is lost across the boundary of $V$. Call this boundary $S$. This change in mass is given by

$$\delta M = -\int_S \rho \mathbb{u}\cdot\mathbb{n}\ dS$$

Putting these facts together we get

$$\frac{d}{dt}\int_V \rho \ dV = -\int_S \rho \mathbb{u}\cdot\mathbb{n}\ dS$$

Using the divergence theorem on RHS and the fact that $V$ is fixed in space on LHS we get

$$\int_V \frac{\partial \rho}{\partial t} dV = -\int_V\nabla\cdot(\rho \mathbb{u})\ dV$$

But $V$ was arbitrary so we get

$$\frac{\partial \rho}{\partial t}+\nabla\cdot(\rho\mathbb{u}) = 0$$

You can rewrite this in terms of a total derivative (exercise) and get

$$\frac{d\rho}{dt}+\rho\nabla\cdot\mathbb u = 0$$

So if the density is conserved (i.e. constant along the flow) then we know from the conservation of mass that

$$\nabla\cdot\mathbb{u} = 0$$

This is just the condition for a fluid to be incompressible. Intuitively that sounds about right.

Note that an incompressible fluid doesn't necessarily have to have uniform density everywhere! It's just got to be constant along the flow. See also Wikipedia.

Further Reading

If you want to understand more about the applications of material derivatives, I suggest you try reading these lecture notes.