To reconstruct sea-level history from changes in tidal environments using diatom assemblages, we need to better understand the relations among brackish diatom assemblages and changing environments along elevational gradients from diverse coastal sites. Our statistical analysis reveals relations between environmental variables and brackish benthic diatom assemblages in the little studied region of south-central Chile. Along four transects across salt marshes at two sites, we identified 224 diatom taxa in 112 samples. Detrended canonical correspondence analysis showed that tidal exposure time index and salinity were appropriately regressed against the abundance of diatom species using unimodal-based methods. Our tests of classical and inverse regressions of weighted average and weighted averaging partial least squares (WA-PLS) showed that WA-PLS resulted in the highest coefficient of determination and the lowest root-mean square of the error of prediction. Our regression will be useful in reconstructing environmental variables from fossil diatom assemblages in Chile.