This study analyzed the speciation and bioavailability of phosphorus in surface sediments from the Orinoco River and Castillero Lagoon (Venezuela), aiming to identify mechanisms of phosphorus retention or release and to establish functional patterns in tropical lotic and lentic systems. Physicochemical analyses, molar ratios, Pearson correlations, and principal component analysis (PCA) with a spatial approach were applied. In the Orinoco River, phosphorus fractions followed the order: detrital phosphorus (79.11 μg/g) > organic phosphorus (17.27 μg/g) > Fe-bound phosphorus (4.78 μg/g) > calcium-bound phosphorus (3.19 μg/g). In Castillero Lagoon, concentrations were higher: detrital phosphorus (154.25 μg/g) > organic phosphorus (70.82 μg/g) > calcium-bound phosphorus (5.78 μg/g) > Fe-bound phosphorus (4.81 μg/g). These results indicate that the Orinoco River is characterized by sandy sediments, low organic matter content, and a predominance of phosphorus in relatively immobile inorganic forms, resulting in low bioavailability (BDP: 22.05 μg/g) and a high N/P ratio (16.22), indicative of phosphorus limitation. In contrast, Castillero Lagoon exhibited fine-grained sediments, high levels of active organic matter, and an accumulation of mobile phosphorus fractions, with higher bioavailability (BDP: 75.63 μg/g) and a low N/P ratio (5.46), a condition consistent with potential eutrophic states. In conclusion, the Orinoco River functions as a geochemical sink of phosphorus, while Castillero Lagoon represents a trophically unstable system, vulnerable to internal phosphorus release. These findings highlight the need for adaptive and spatially explicit management strategies in tropical aquatic ecosystems.