Carbonate rocks, particularly reefs and circum-reef facies, are significant reservoir rocks whose reservoir properties depend on their primary composition and diagenetic history. This paper reconstructs the influence of multistage selective diagenesis on the pore system evolution and porosity-permeability properties of the Anisian tropical reef system (Karchowice and Diplopora Beds) in the Muschelkalk of Upper Silesia, southern Poland, using field and slab observations, standard and cathodoluminescence petrography, bulk and SIMS carbon and oxygen stable isotope analyses, porosity-permeability plug study, and computer image analysis of macroporosity (> 5 mm across). The reef system comprises two distinct levels of sponge-microbial(-coral) reef mounds surrounded by diverse bioclastic, peloidal, coated-grain, and micritic facies rich in Balanoglossites burrows. The strata experienced complex diagenetic alterations related to various fluids (marine, evaporitic, meteoric) and diagenetic environments (shallow substratal, burial, telogenetic), including (in chronological order): 1) early-marine precipitation of isopachous fibrous rims; 2) early dissolution during emersion; 3) brine-reflux dolomitization; 4) patchy silicification; 5) recrystallization; 6) burial calcite cementation by heated marine fluid; 7) deposition of vadose silt; 8) meteoric calcite cementation; 9) chemical compaction; 10) fracturing; and 11) final karstification, dedolomitization, FeO precipitation, and Liesegang ring formation by meteoric water during Cenozoic telogenesis. Many processes were selective and affected the same (more permeable) parts of the rocks. The strata exhibit porosities reaching 50% (combined plug porosity of 6–35% and macroporosity of up to 20%) and plug permeabilities of 0.07–70 mD, with the highest values occurring in the reefs and burrowed facies. The dominant late-stage telogenic dissolution pores originated from selective removal of dolomitized micrite within burrows and between sponge-microbial automicrite as well as dolomite crystals. The study illustrates the transition of the reef system from tight to porous due to multistage selective diagenesis and fluid flow, which enhanced subtle permeability differences between various types of micrite. This is the first case where four different fluids (dolomitizing, early dissolving, calcite-forming, and late dissolving) selectively migrated through the same rock parts at different times and modified them one after another.