Spatial and temporal variability in the reproductive output of marine invertebrates affects individual energy balance and physiology, reproductive evolution, and population connectivity and recruitment. Multiple factors modulate reproductive investment and generate temporally varying or persistent spatial patterns across different scales. We used a hierarchical sampling design at 4 spatial scales over 2 consecutive years to characterize spatial patterns in the intertidal mussel Perumytilus purpuratus along 600 km of central Chile. The gonadosomatic index (GSI) and the condition index were assessed in monthly samples collected during peak reproduction. No latitudinal trends or regional breaks were observed across the region. The largest fraction of variability was explained by differences among localities, separated by 10s of kilometers, and among individuals, spaced a few centimeters to meters apart. Intermediate spatial scales, i.e. few kilo meters or 100s of meters, explained only small fractions of the total variance. Persistent variability at the scale of locality is understood as resulting from topographic modulation of upwelling intensity over mesoscales. Variability among individuals is interpreted as variation in both microenvironmental and individual hormonal conditions. Sea surface temperature, chlorophyll a, and upwelling intensity were not correlated with GSI across space. Our results are consistent with the idea that a suite of variables, rather than a single dominant factor, modulate reproductive output and generate environmental mosaics over 10s of kilometers. Observed spatio-temporal patterns also suggest that spatial variability in larval output may have important consequences on metapopulation dynamics and that territory-based conservation of reproductive stock can be an effective management strategy.