Drawing from the experience of the Limpopo River Basin in Mozambique, the paper analyses the articulation of a water rights framework in the context of decentralised river basin governance and IWRM-inspired reforms. The nexus between financial autonomy, service provision, stakeholder participation and the resultant allocation of water within the river basin is explored by scrutinising the newly instituted system of water permits and payments. Three cases are examined: (1) parastatal agencies managing large perimeters of irrigated land; (2) large-scale commercial companies irrigating land; and (3) so-called focal points representing groups of smallholder irrigators. The three presented cases show that structural challenges, local geographies and power relations shape the final outcome of water reforms in relation to decentralised river basin management, stakeholders' participation and accountability. Rather than improving accountability to users and securing the financial basis for sustainable infrastructure operation and maintenance, the permit system in place reinforces existing inequalities.