<p>We relate the counting of refined BPS numbers on compact elliptically fibred Calabi-Yau threefolds <i>X</i> to Wilson loop expectations values in the gauge theories that emerge in various rigid local limits of the 5d supergravity theory defined by M-theory compactification on <i>X</i>. In these local limits <i>X</i>_∗ the volumes of curves in certain classes go to infinity, the corresponding very massive M2-brane states can be treated as Wilson loop particles and the refined topological string partition function on <i>X</i> becomes a sum of terms proportional to associated refined Wilson loop expectation values. The resulting ansatz for the complete refined topological partition function on <i>X</i> is written in terms of the proportionality coefficients which depend only on the <i>ϵ</i> deformations and the Wilson loop expectations values which satisfy holomorphic anomaly equations. Since the ansatz is quite restrictive and can be further constrained by the one-form symmetries and E-string type limits for large base curves, we can efficiently evaluate the refined BPS numbers on <i>X</i>, which we do explicitly for local gauge groups up to rank three and <i>h</i>₁₁(<i>X</i>) = 5. These refined BPS numbers pass an impressive number of consistency checks imposed by the direct counting of these numbers using the moduli space of one dimensional stable sheaves on <i>X</i> and give us numerical predictions for the complex structure dependency of the refined BPS numbers.</p>