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Crocodyliforms are an extant group of highly successful pseudosuchian archosaurs. However, their macroevolutionary history remains poorly understood, partly as a result of heterogeneous sampling of their fossil record, which obscures genuine biological patterns. Here, we focus on their diversity dynamics through the Late Jurassic and Early Cretaceous, a relatively neglected period in crocodyliform history that witnessed the demise (e.g., the marine Thalattosuchia) and apparent radiation (e.g., the terrestrial Notosuchia) of major lineages. We take a combined approach to reconstructing their diversity via application of shareholder quorum subsampling (SQS) on a newly compiled and comprehensive fossil occurrence dataset (919 occurrences of 228 genera), as well as producing a phylogenetic diversity estimate (PDE) using a newly constructed and well-sampled (270 species) informal supertree. There is strong evidence for a substantial decline in total crocodyliform diversity through the Jurassic/Cretaceous (J/K) boundary, with terrestrial forms (including semi-aquatic taxa) suffering a more severe extinction than marine taxa. Marine genera show either a diversity decline through the J/K boundary (PDE), or a slight increase (SQS), although much of the Early Cretaceous is too poorly sampled for SQS to produce reliable diversity estimates. Extinction rates were highest in the latest Jurassic, and origination rates remained depressed through the Early Cretaceous. The responses of marine and terrestrial crocodyliforms to this extinction are decoupled; whereas marine taxa did not recover to pre-Cretaceous levels of diversity, terrestrial taxa rapidly recovered and exceeded pre-Cretaceous diversity. After accounting for serial autocorrelation in a range of environmental time series data, we fitted maximum-likelihood models to identify factors that might have driven our recovered diversity and extinction patterns. A combination of eustatic sea-level changes and perturbations to the marine sulphur cycle are primarily responsible for crocodyliform macroevolutionary dynamics through the Jurassic to Cretaceous interval. It is likely that these two factors are related, with a sea-level lowstand through the J/K boundary responsible for increasing sulphur toxicity, although we cannot rule out that climatic variability (e.g., a broad aridity belt covering the low latitudes of the Southern Hemisphere), or increasing volcanic activity (e.g., emplacement of the Paraná-Etendeka flood basalts), might also have played a role.