Extraction of filamentous algae from river pools is highly effective for the control of Anopheles pseudopunctipennis in southern Mexico. We determined the magnitude of changes to the aquatic insect community following single annual perturbations performed over two years. In 2001, algae were manually removed from all the pools in a 3 km long section of the River Coatán, Mexico, while an adjacent section was left as an untreated control. In 2002, the treatments of both zones were switched and algal extraction was repeated. The abundance of An. pseudopunctipennis larvae pupae was dramatically reduced by this treatment and remained depressed for two to three months. A total of 11,922 aquatic insects from ten orders, 40 families, and 95 genera were collected in monthly samples taken over five months of each year. Algal extraction did not reduce the overall abundance of aquatic insects in river pools, but a greater abundance and a greater richness of taxa were observed in 2002 compared to the previous year. This was associated with reduced precipitation and river discharge in 2002 compared to 2001. Shannon diversity index values were significantly depressed following algal extraction for a period of three months, in both years, before returning to values similar to those of the control zone. However, differences between years were greater than differences between treatments within a particular year. When insects were classified by functional feeding group (FFG), no significant differences were detected in FFG densities between extraction and control zones over time in either year of the study. Similarly, percent model affinity index values were classified as “not impacted” by the extraction process. Discriminant function analysis identified two orders of insects (Diptera and Odonata), water temperature, dissolved oxygen and conductivity, and river volume (depth, width, and discharge) as being of significant value in defining control and treatment groups in both years. We conclude that habitat manipulation represents an effective and environmentally benign strategy for control of An. pseduopunctipennis. Variation in precipitation and river discharge between years was much more important in determining aquatic insect community composition than variation generated by the filamentous algal extraction treatment.