The tilapiine cichlids Oreochromis leucostictus and Tilapia zillii were introduced into Lake Naivasha, Kenya, in 1956. Previous studies on data collected to 1987 revealed they were persistent following establishment, despite environmental variability and exploitation. Recent data, however, suggest this persistence is under threat as data indicate some significant declines in aspects of their abundance since 1999. The influence of changes in lake level, allodiversity and fishing effort on this decline was tested and showed that a decline in lake level was a significant causal factor. The recent change in allodiversity, with the establishment and dominance of Cyprinus carpio in the fishery, was not significant on the catch per unit effort of O. leucostictus but was on T. zillii. Since 1999, catches of tilapiines in the fishery have been independent of fishing effort, contrary to between 1975 and 1987, suggesting their management through application of fishery models may no longer be applicable. As it was anthropogenic-mediated lake level changes that were mainly responsible for their decline, then lake management should focus on sustainable water utilization that maximizes lake levels in accordance with the basin-wide water balance.