Abstract Large microalgae, such as diatoms can generate high levels of biomass, unlike small phytoplankton components in the austral fjords and estuarine systems of Chile. We propose a cell-size-based diversity index ( H ′ size ) measured as chlorophyll-a concentrations (Chl-a) to determine if the relationship between H ′ size versus Chl-a results in a hump-shaped distribution considering: (i) the intermediate disturbance hypothesis, (ii) phytoplankton size colonization strategies, and (iii) predictions of low H ′ size with high or low Chl-a levels and peaks in H ′ size with intermediate Chl-a levels. The functional responses of phytoplankton are tightly coupled to environmental conditions. Could, then, the relationship between H ′ size and Chl-a occur on a particular temporal/spatial scale? Herein, we analyze data from three CIMAR-Fiordos cruises performed between 2001 and 2002 within areas of different continental influence from 41° to 47°S. Phytoplankton samples were taken at different locations and depths, filtered to obtain Chl-a with and without size-fractionation (>20 μm, H ′ size . Total Chl-a (TChl-a) changed by two orders of magnitude between different cruises and areas. The small phytoplankton fraction ( 20 μm) with high TChl-a values (≥1 mg m–3). Although other relationships can be found on smaller scales, we determined unimodal (hump-shaped) relationships through quadratic quantile regressions between the H ′ size index and TChl-a and between H ′ size or TChl-a and the abiotic factors when considering data from all three cruises and areas. H ′ size versus TChl-a was driven by one variable or by different combinations of variables, and according to low–high disturbance level: high TChl-a and larger size classes predominated in deeper upper mixed layers having higher light availability, whereas shallower upper mixed layers with lower light availability presented lower TChl-a and predominantly smaller cell size classes. Thus, the larger temporal/spatial scales used here allowed us to test the hypothesis of the unimodal expression of phytoplankton patterns in these coastal ecosystems.