In the northern Colombian Caribbean the main fishing activity for hundreds of artisanal fishermen is based upon small pelagic fish. The stock assessment has been done only sporadically by means of hydro-acoustic research surveys. We analyse here the information collected from a new hydro-acoustic survey carried out in 1997 by using the intrinsic theory of geostatistics, as applied to four stocks of small pelagic fish, three of them under exploitation at the moment of the survey (Atlantic thread herring: Opisthonema oglinum, round sardinella: Sardinella aurita, and scad: Decapterus punctatus), and a fourth one (scaled herring: Harengula jaguana) in an exploratory fashion. The relation between some habitat features (temperature, salinity, and oxygen concentration) and fish density was studied by using a randomisation technique. Clear spatial autocorrelation was discerned for all four fish species using the experimental variogram, either the classic or a robust version. The Atlantic thread herring stock was divided into two different groups, one of smaller/younger fish from the south and another of older/larger fish from the north, leading to five separate geostatistical analyses. Omni-directional spherical variograms were appropriate model descriptions of experimental variograms for all four fish species. For all five analyses: (1) low or moderate residual variance was left in the nugget parameter, indicating a good spatial resolution of the observations; (2) the range parameter closely matched the variation in the width of the continental shelf, suggesting that the size of the groups was determined by large-scale habitat features; (3) cross-validation analysis revealed very low bias during kriging, pointing to adequate spatial continuity modelling. Surprisingly, by far the most abundant species was the scaled herring, followed by the main fishing target Atlantic thread herring. A single large and dense scaled herring patch accounted for half of the total assessed biomass. There were clear spatial differences between the two patches of Atlantic thread herring: patches of large-sized (northern) Atlantic thread herring accumulate most of the biomass and are larger in spatial extension but more homogeneous in density than patches of small-sized (southern) fish. The other two species showed only marginal abundance. There were clear relations between measured habitat features and fish local abundance. Scaled herring stock was associated with a narrow range of cold waters. Atlantic thread herring fish were associated with the upwelled waters in the northern area. This patch elongated offshore in apparent response to upwelling. The younger Atlantic thread herring patch was associated with warmer waters, far from the upwelling area.