Intermittent streams are characterized by significant periods of low to no flow, yet are also frequently subjected to flashy, high floods. Floods alter ecosystem function and result in variable successional patterns across the stream network. Yet, the timing of restored function after floods in intermittent stream networks is relatively unexplored. We measured recovery of stream ecosystem function using rates of gross primary production (GPP), ecosystem respiration (ER), net ecosystem production (NEP), and the primary production to respiration ratio (P/R) across eight locations in the Kings Creek drainage basin with differing preflood conditions (previously dry [intermittent] or flowing [perennial]) over a 30-d period following a 2-yr return interval flood. We found that all metabolic rates (GPP, ER, NEP, P/R) varied primarily by time (days since flood) and antecedent flow, but not spatial network position (i.e., drainage area). Intermittent sites exhibited high rates of ER (0.17–3.33 g dissolved oxygen [DO] m−2 d−1) following rewetting compared to perennial sites (0.03–1.17 g DO m−2 d−1), while GPP, NEP, and P/R were slower to recover and varied less between sites of differing preflood conditions. Metabolic rates were not strongly influenced by other environmental conditions. A large proportion of variation was explained by the random effect of location. Our results suggest that metabolism is temporally asynchronous and highly heterogenous across intermittent watersheds and that antecedent hydrology (drying prior to rewetting) stimulates heterotrophic activity, likely dependent on terrestrially derived organic matter and nutrient subsidies.