The ability of nutrient enrichment bioassays versus physiological indicators to detect ecosystem changes in nutrient cycling were compared. Field data spanned four years in three lakes, two of which were subjected to fish manipulations in year two. The manipulations changed phytoplankton and zooplankton assemblages and nutrient cycling. Phosphorus and nitrogen enrichments (phosphorus enrichment bioassay (PEB), nitrogen enrichment bioassay, nitrogen plus phosphorus enrichment bioassay, specific alkaline phosphatase activity, ammonium enhancement response, and total nutrients (total phosphorus, total nitrogen) were measured before and after the manipulations. Although physiological indicators were often more sensitive, nutrient enrichments and physiological indicators both led to the same conclusions regarding changes in nutrient cycling. Total nutrients did not respond to manipulation. Physiological indicators measure the extant algal assemblage, are rapidly assayed, can be run more frequently than nutrient enrichments, and lead to the same conclusions as nutrient enrichment bioassays.