Both nitrogen (N) and phosphorus (P) can limit primary production in shallow lakes, but it is still debated how the importance of N and P varies in time and space. We sampled 83 shallow lakes along a latitudinal gradient (5 degrees 55 degrees S) in South America and assessed the potential nutrient limitation using different methods including nutrient ratios in sediment, water, and seston, dissolved nutrient concentrations, and occurrence of N-fixing cyanobacteria. We found that local characteristics such as soil type and associated land use in the catchment, hydrology, and also the presence of abundant submerged macrophyte growth influenced N and P limitation. We found neither a consistent variation in nutrient limitation nor indications for a steady change in denitrification along the latitudinal gradient. Contrary to findings in other regions, we did not find a relationship between the occurrence of (N-fixing and non-N-fixing) cyanobacteria and the TN:TP ratio. We found N-fixing cyanobacteria (those with heterocysts) exclusively in lakes with dissolved inorganic nitrogen (DIN) concentrations of < 100 microg/L, but notably they were also often absent in lakes with low DIN concentrations. We argue that local factors such as land use and hydrology have a stronger influence on which nutrient is limiting than climate. Furthermore, our data show that in a wide range of climates N limitation does not necessarily lead to cyanobacterial dominance.