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Sentinel-2 offers great potential for monitoring water quality in inland and coastal waters. However, atmospheric correction in these waters is challenging, and there is no standardized approach yet, but different methods coexist under constant development. The atmospheric correction Case 2 Regional Coast Colour (C2RCC) processor has been recently updated with the C2X-COMPLEX (C2XC). This study is one of the first attempts at exploring its performance, in comparison with C2RCC and C2X, in inland and coastal waters in the east of the Iberian Peninsula, in retrieving water surface reflectance and estimating chlorophyll-a ([Chl-a]), total suspended matter ([TSM]), and Secchi disk depth (ZSD). The relationship between in situ ZSD and Kd_z90max product (i.e., the depth of the water column from which 90% of the water-leaving irradiance is derived) of the C2RCC processors demonstrated the potential of this product for estimating water clarity (r > 0.75). However, [TSM] and [Chl-a] derived from the different processors with default calibration factors were not suitable within the targeted scenarios, requiring recalibration based on optical water types or a shift to dynamic algorithm blending approaches. This would benefit from switching between C2RCC and C2XC, which extends the potential for improving surface reflectance estimates to a wide range of scenarios and suggests a promising future for C2-Nets in operational monitoring of water quality. Jesús Soriano held a pre-doctoral grant funded by Agència de Gestió d’Ajuts Universitaris i de Recerca (2020FI_B2 00148). Esther Patricia Urrego holds a pre-doctoral grant funded by Ministerio de Ciencia, Innovación y Universidades (PRE2019-088232). This research was partially funded by the European Union—ERDF and the Ministry of Science and Innovation and the State Research Agency of Spain under project RTI2018-098651-B-C51 (FLEXL3L4—Advanced Products L3 and L4 for the FLEX-S3 mission).