Biosiliceous sedimentary rocks are well known from the geologic record and many are correctly interpreted to have formed in deep-water or cold-water environments. Shallow non-polar spiculites are also known from the rock record, yet no modern analog has been documented for such environments. Bathurst Harbour, an estuarine system in southwest Tasmania, provides this much-needed modern analog. In this system a sharp halocline separates tannin-rich low-salinity surface waters from clear marine bottom waters. Tannins supply few nutrients and substantially reduce light penetration to bottom environments, resulting in a thinned photic zone and the mixing of deeper-water sub-photic biotas of soft corals, bryozoans, and sponges with other organisms more typical of this temperate shallow-water environment. The well-defined halocline allows a typically marine biota, including echinoderms, to live in bottom waters of this estuarine setting. The bioclastic factory, producing both carbonate and siliceous particles, exists in marine subphotic bottom waters of incised channel and shallow rocky environments along the shoreline. Extensive organic-rich soft sediments in protected embayments generate few bioclasts, but contain allochthonous sponge spicules transported from the adjacent bioclastic factory. Trapping of organic material within the estuarine system lowers sediment pH and promotes dissolution of carbonate biofragments, resulting in preferential preservation of siliceous sponge spicules. This situation implies that many biosiliceous neritic deposits in the rock record may be the result of similar preferential preservation.