Streams in the Hondo River basin (Mexico-Belize) face ecological disturbances caused by use of fertilizers and pesticides, as well as invasion by exotic species. These threats can affect ecosystem functioning, with loss of biotic integrity. Mass-balance trophic models were developed to quantify the energy flow and assess the maturity and health states for three locations in the basin, in two seasons. Quantitative sampling was carried out for plankton, fish, macrobenthos, insects, benthic autotrophs, detritus, and exported organic matter. Field sampling was supplemented with a literature review to define functional groups and their diets. Results showed that more than 50% of the energy flow originated from detritus, which suggests that the systems are bottom-up controlled. Low values of energy transfer efficiency, connectivity, omnivory, recycling, mean path length, and ascendency suggest that the freshwater bodies in this basin are oligotrophic, but they are not in a good health and thus have low stability and are susceptible to disturbance, despite the fact that they also have a high number of specialized functional groups, indicative of a well-organized food web, supposed to be representative of healthy ecosystems. The potential of these models to manage shallow tropical streams is discussed.