Relative div is passing over fixed div while scrolling

I think what you are looking for is the CSS property z-index. See here for documentation: http://reference.sitepoint.com/css/z-index

I threw together a small example showing how to use it with your CSS: http://jsfiddle.net/B63Km/

The basic idea is the higher the z-index, the closer the element is to you.

Hi I think you should do this:

css

#navcontainer
{
    position:fixed;
    background:red;
    left:0;
    right:0;
    top:0;
    height:100px;
    z-index:3;
}

.city
{
    position:relative; 
    background:green;
    left:0;
    right:0;
    padding:10px;
    top:100px;
    z-index:2;
}

.city .text 
{
    padding:10px;
    background:yellow;
}​

HTML

<div id="navcontainer">This is navigation</div>

<div class="city">
    <div class="text">here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br />here text <br /></div>
</div>
​

Live demo http://jsfiddle.net/xLnKN/1/

How can you avoid using a z-index for this? Z-index is typically considered an anti-pattern and can easily snowball into requiring other elements to also require z-index.

Use a higher z-index for the header div, ie., city and a lower one for the below div (ie., the relative one)