The number of recreational/non-elite athletes participating in marathons is increasing, but data regarding impact of endurance exercise on cardiovascular health are conflicting. This study evaluated 79 recreational athletes of the 2016 Barcelona Marathon (72% men; mean age 39 ± 6 years; 71% ≥35 years). Blood samples were collected at baseline (24–48 h before the race), immediately after the race (1–2 h after the race), and 48-h post-race. Amino-terminal pro-B type natriuretic peptide (NT-proBNP, a marker of myocardial strain), ST2 (a marker of extracellular matrix remodeling and fibrosis, inflammation, and myocardial strain), and high-sensitivity troponin T (hs-TnT, a marker of myocyte stress/injury) were assayed. The median (interquartile range, IQR) years of training was 7 (5–11) years and median (IQR) weekly training hours was 6 (5–8) h/week, respectively. The median (IQR) race time (h:min:s) was 3:32:44 (3:18:50–3:51:46). Echocardiographic indices were within normal ranges. Immediately after the race, blood concentration of the three cardiac biomarkers increased significantly, with 1.3-, 1.6-, and 16-fold increases in NT-proBNP, ST2, and hs-TnT, respectively. We found an inverse relationship between weekly training hours and increased ST2 (p = 0.007), and a direct relationship between race time and increased hs-TnT (p < 0.001) and ST2 (p = 0.05). Our findings indicate that preparation for and participation in marathon running may affect multiple pathways affecting the cardiovascular system. More data and long-term follow-up studies in non-elite and elite athletes are needed.