There is considerable theoretical and practical interest in verifying equilibrium conditions in wetlands and other natural systems that have been disturbed or displaced by anthropogenic stress. Similarly, determination of equilibrium conditions in alternative or reclaimed ecosystems, such as wetlands created to replace terrestrial ecosystems following surface mining, is a necessity for regulation and management of newly created systems. An important question for alternative ecosystems is "do equilibrium conditions resemble those of ecologically similar natural systems in the same geographic area?" We have used community structure and colonization dynamics of aquatic, eukaryotic microorganisms for this purpose. Photosynthetic species such as motile algae integrate the effects of variations in water quality and are especially reflective of nutrient levels. Heterotrophic forms crop bacteria and process detrital materials and reflect the relative state of detrital processing in sediments. In studies of 21 natural and reclaimed Florida lakes, we found that microbial colonization of artificial substrates could be used to estimate recovery rates of lakes following reclamation activities. Microbial community structure differed in the youngest lakes studied, but lakes greater than two years old showed little difference from natural lakes in terms of community composition or colonization dynamics. Young lakes had high levels of aluminum and selenium and low pH. Microbial species are sensitive to unnatural disturbances such as inputs of excessive nutrients or toxic substances and can provide one type of evidence for ecosystem recovery following stress.