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Abstract Studies of annual patterns of ecosystem metabolism in rivers have primarily been conducted in temperate ecosystems, and little is known about metabolic regimes of tropical rivers. We estimated ecosystem metabolism in four nonwadeable rivers in southern México that varied in size and the extent of human disturbance. The smaller rivers with limited human disturbance showed reduced gross primary production (GPP; 1.0 and 1.7 g O₂m⁻² d⁻¹), ecosystem respiration (ER; − 1.9 g O₂m⁻²d⁻¹), and net ecosystem production (NEP) approaching autotrophy (− 0. 8 and − 0.3 g O₂m⁻²d⁻¹) relative to rivers draining larger, more disturbed catchments (GPP, 1.2 and 2.7 g O₂m⁻²d⁻¹; ER, − 5.7 and − 6.9 g O₂m⁻²d⁻¹; NEP, − 3.8 and − 3.7 g O₂m⁻²d⁻¹). In all rivers, GPP and ER varied seasonally with discharge. The smaller rivers exhibited a distinct pattern of greater and sustained GPP during periods of low discharge, a seasonal metabolic regime we describe as “flow decline.” In general, process–discharge relationships exhibited thresholds, with an initial decline in GPP and ER, with increasing discharge and an increase in ER at higher flows. Relative to larger and more disturbed watersheds, smaller rivers showed a more constrained metabolic fingerprint. Annual NEP (− 1033 and − 641 g C m⁻² yr⁻¹) in the larger rivers was more negative than the global average, supporting evidence from other studies that tropical rivers are greater contributors to CO²emissions than temperate ecosystems. Our study indicates that hydrological seasonality is a major driver of metabolism in tropical rivers.