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For practical applications, wireless sensor networks (WSNs) with diverse sensor types and that run heterogenous applications are becoming increasingly important. Our motivation in this work is to, for this sort of heterogenous WSNs, devise a flow control and resource allocation algorithm (with respect to both wireless channel usage and sensor node energy), that allow data to be gathered in the fairest manner, while still respecting the needs of different sensing tasks. A two-layer hierarchical transport architecture is designed to guarantee a certain measure of optimality in rate allocation, addressing the balance between fairness and performance. In essence, utility max-min fairness is achieved among upper-layer cluster heads, whereas utility proportional fairness is achieved within each lower-layer cluster. The proposed architecture is to be applied to a real marine sensor network on the Great Barrier Reef.