Changes in circulation associated with the shoaling of the Isthmus of Panama and the Caribbean carbonate crash in the Miocene were investigated using Nd isotopes from fossil fish teeth and debris from two sites in the Caribbean Basin (Ocean Drilling Program Sites 998 and 999) and two sites in the eastern equatorial Pacific (Sites 846 and 1241). The total range for ϵNd values measured from 18 to 4.5 Ma in the Caribbean is −7.3 to 0. These values are higher than Atlantic water masses (~–11) and range up to values equivalent to contemporaneous Pacific water masses, confirming that flow into the Caribbean Basin was composed of a mixture of Pacific and Atlantic waters, with an upper limit of almost pure Pacific-sourced waters. Throughout the Caribbean record, particularly during the carbonate crash (10–12 Ma), low carbonate mass accumulation rates (MARs) correlate with more radiogenic ϵNd values, indicating increased flow of corrosive Pacific intermediate water into the Caribbean Basin during intervals of dissolution. This flow pattern agrees with results from general ocean circulation models designed to study the effect of the shoaling of the Central American Seaway. Low carbonate MARs and high ϵNd values also correlate with intervals of increased Northern Component Water production and, therefore, enhanced conveyor circulation, suggesting that the conveyor may respond to changes in circulation associated with shoaling of the Central American Seaway. Reduced Pacific throughflow related to shoaling of the seaway led to a gradual increase in carbonate preservation and more Atlantic-like ϵNd values following the carbonate crash.