Lake chemistry is influenced by land use in the surrounding watershed, particularly in complex urban landscapes, which are commonly subjected to an increase in material loadings. Because land use is rarely uniform, individual ecosystems embedded within the landscape may reflect varying water quality conditions. The Lake Merced system is composed of three lake basins with watersheds (surface area = 13 km2) residing entirely within the city of San Francisco, California. On nine occasions from January-June 1995 we sampled the two main lakes (North and South Lake Merced) within the system to evaluate their relative productivity and nutrient status. On each date, several physical-chemical conditions were measured, and nutrient enrichment bioassays were performed to evaluate the nutritional status of the phytoplankton (nitrogen (N) and phosphorus (P) enrichment in a 2 × 2 factorial experimental design). All the parameters tested except temperature were higher in the north lake compared with the south (pair-wise Wilcoxon Ranked sums), and common trophic state variables were more than 2-fold higher in the north lake. Phytoplankton growth in North Lake Merced was N-limited while growth in South Lake Merced was co-limited by N and P. In sum, our data indicate that differences among these lakes may be explained by simple volume differences between lakes (with the smaller North Lake Merced being more eutrophic), and heavy stocking of fishes to the north lake. Particulate nutrient ratios (N:P) were good indicators of phytoplankton nutritional status throughout the system, while N:P ratios based on total nutrient concentrations gave misleading results.