Cyathostomins are the most prevalent equine intestinal parasites and resistance has been reported in these nematodes against all 3 licensed anthelmintic classes. Strategies need to be developed that are less dependent upon drugs and more reliant on management-based control. To develop these we need to understand natural transmission patterns better. Here, we analysed longitudinal fecal egg count (FEC) data from 5 pony populations used for conservation purposes. We tested how egg excretion varied amongst populations and individuals, and how this was affected by age and climate. There was evidence for consistency in FECs over time at the individual level; this was generally weak and accounted for <10% of the total variance. Animals <5 years old had higher FECs and there was profound seasonal variation in FECs, with highest levels recorded in spring/summer. Effects of monthly temperature and rainfall explained most, but not all, of the observed seasonal variation and associations between climate measures and FECs were stronger in younger versus adult animals. One population was occasionally treated with anthelmintics and analysis of this population suggested that treatment substantially altered the seasonal dynamics. This paper highlights the variability in strongyle egg excretion amongst individuals and the factors involved in this variation.