Surface water colors naturally vary depending its content in organic matter (humic and fulvic acids). Other mineral factors (like iron or manganese precipitation) may also affect the color of water.
There are many reasons, but many of them are based on the substances dissolved in water that have differential selective absorption of light. Red wavelengths are filtered out quickly, but the shorter blue wavelengths have deeper penetration. Substances affect their depth penetration.
The yellow to brown color is caused by large and complex organic substances which are mainly derived from decomposing plants and animals. To some extent the color may also originate from secretions by microorganisms, plants and animals.