Communication requirements for cognitive radio sensor networks (CRSN) necessitate addressing the problems posed by dynamic spectrum access (DSA) in an inherently resource-constrained sensor networks regime. In this paper, arising challenges for reliability and congestion control due to incorporation of cognitive radio capability into sensor networks are investigated along with the open research issues. Impact of DSA, i.e., activity of licensed users, intermittent spectrum sensing and spectrum handoff functionalities based on spectrum availability, on the performance of the existing transport protocols are inspected. The objective of this paper is to point out the urgent need for a novel reliability and congestion control mechanism for CRSN. To this end, CRSN challenges for transport layer are revealed and simulation experiments are performed to demonstrate the performance of the existing transport protocols in CRSN.