SEAMLESS has the strong ambition to develop novel ensemble data assimilation systems exploitable operationally in the CMEMS MFCs, in some cases as alternative of established variational methods. The rationale is to improve the estimation of key marine ecosystem indicators. The objectives of this document are: (i) to report on the developments of ensemble assimilation methods and assimilation experiments performed in SEAMLESS, and (ii) to provide methodological guidelines to assess the observability and controllability of the target indicators across the CMEMS MFC 3D domains using common probabilistic evaluation tools.