Coral reef growth is primarily determined by constructive and bioerosive processes acting on key reef-building organisms. Among them, corals are major contributors to the construction of reef frameworks, while crustose coralline algae (CCA) primarily take part in reef cementation. Despite the significance of CCA for reef ecology and functioning, there is very little information on CCA bioerosion rates, in particular in reefs influenced by coastal upwelling. Therefore, the aim of this study was to examine the percentage and rates of internal bioerosion by macroborer invertebrates in two dominant CCA species and to explore whether the oceanographic variability influences the nature of bioerosion in coral reefs of the Tayrona Natural National Park (Colombian Caribbean). Annual rates of gross calcium carbonate production for Lithoplyllum kaiseri and Porolithon antillarum were 0.556 (± 0.38) and 0.883 (± 1.0) g CaCO3 cm−2 year−1, respectively, and estimates of percent area covered by macroborer boreholes showed values of 29.7% for L. kaiseri and 18.0% for P. antillarum. Rates of calcium carbonate removal by internal macroborers in L. kaiseri (0.19 ± 0.17 g CaCO3 cm−2 year−1) were higher than those in P. antillarum (0.14 ± 0.17 g CaCO3 cm−2 year−1). The percentage of internal bioerosion did not vary significantly across climatic/oceanographic seasons. Boreholes produced by mollusks, polychaetes, sponges and sipunculids were identified, with mollusks having the highest erosion activity. A total of 2,095 individuals of boring and opportunistic organisms were identified and grouped into 29 families (17 polychaetes, 4 mollusks, 2 sipunculids and 6 crustaceans). The composition of the macroborer invertebrate community also varied between CCA species, with higher boreholes attributed to vermetids in L. kaiseri than in P. antillarum. Although there is no clear influence of climatic seasons on internal bioerosion, the high rates of CCA bioerosion may reduce reef consolidation in the region.