Cryptosporidium continues to be problematic for the water industry, with risk assessments often indicating that treatment barriers may fail under extreme conditions. However, risk analyses have historically used oocyst densities and not considered either oocyst infectivity or species/genotype, which can result in an overestimation of risk if the oocysts are not human infective. We describe an integrated assay for determining oocyst density, infectivity, and genotype from a single-sample concentrate, an important advance that overcomes the need for processing multiple-grab samples or splitting sample concentrates for separate analyses. The assay incorporates an oocyst recovery control and is compatible with standard primary concentration techniques. Oocysts were purified from primary concentrates using immunomagnetic separation prior to processing by an infectivity assay. Plate-based cell culture was used to detect infectious foci, with a monolayer washing protocol developed to allow recovery and enumeration of oocysts. A simple DNA extraction protocol was developed to allow typing of any wells containing infectious Cryptosporidium. Water samples from a variety of source water and wastewater matrices, including a semirural catchment, wastewater, an aquifer recharge site, and storm water, were analyzed using the assay. Results demonstrate that the assay can reliably determine oocyst densities, infectivity, and genotype from single-grab samples for a variety of water matrices and emphasize the varying nature of Cryptosporidium risk extant throughout source waters and wastewaters. This assay should therefore enable a more comprehensive understanding of Cryptosporidium risk for different water sources, assisting in the selection of appropriate risk mitigation measures.C ryptosporidium is ubiquitous in source waters and wastewaters, presenting a treatment challenge on account of its small size, resistance to chlorine disinfection, and the absence of more easily measured surrogates to allow treatment performance validation (1, 2). These characteristics make Cryptosporidium problematic for the water industry, and the ever-present threat from this pathogen requires sound characterization and management of risks, including validation and monitoring of critical control points (3-5). Removal of Cryptosporidium by treatment processes can be highly variable (6), so validation and monitoring of individual processes are important to ensure appropriate performance. Even for validated systems, treatment failure is possible under highly adverse conditions, and management of this risk may require significant capital expenditure to provide sufficient risk mitigation for extreme events. However, risk assessments frequently utilize historical monitoring data based on total oocyst numbers, not considering either oocyst infectivity or species/genotype, resulting in possible overestimation of risk.Of the greater than 26 species or genotypes of Cryptosporidium that might be detected in the environment, only C. parvum and C. hominis common...