The number and type of microorganisms present in water bodies determine both their productivity and trophic status. A water body with a lot of photosynthetic organisms (both micro and macro) per unit area is highly productive, usually turbid and with high amounts of nutrients anddissolved oxygen (DO). In contrast, non-productive water bodies have a very low density of organisms per unit area, are fairly transparent and have low nutrient and DO concentrations.

Since microorganisms thrive on nutrients, they are a very useful indicator of how polluted (or full of nutrients) the water body may be.

Usually, the presence of microorganisms in a water body is analysed by taking a sample and observing it under alight microscope.