TermsAggregation topTermAgg = null;
TermsAggregation currentAgg = null;
foreach (var pivotName in activePivots)
{
    newTermAgg = new TermsAggregation("pivot")
    {
        Field = pivot.ToString().ToLower()
    };

    if (topTermAgg == null)
    {
        topTermAgg = newTermAgg;
    }
    else
    {
        currentAgg.Aggregations = newTermAgg;
    }
    currentAgg = newTermAgg;
}

var searchRequest = new SearchRequest(Indices.Index("a", "b", "c"))
{
    Size = 0,
    Aggregations = topTermAgg,
    Query = query,
};

{
  "size": 0,
  "query": {
    "bool": <Fairly complex query, that works fine. It's the aggregation that has the problem.>
  },
  "aggs": {
    "pivot": {
      "terms": {
        "field": "pivot1"
      },
      "aggs": {
        "pivot": {
          "terms": {
            "field": "pivot2"
          }
        }
      }
    }
  }
}