The Smiřický family, one of the wealthiest in Bohemia in the second half of the 16th century, were important owners whose rule over the estate was associated with extensive construction activity. Zikmund Smiřický bought Náchod in 1544, and it remained in the family's possession until 1620, when it was confiscated as part of the post-White Mountain confiscations for the Smiřický family's participation in the Estates Uprising. The last male member of the family, Albrecht Jan, who inherited the Náchod estate in 1614, was an active participant in the Estates Uprising, personally taking part in the Defenestration of May 1618 and serving as one of the thirty directors. However, his promising career was cut short by his unexpected death in November 1618. The extensive Smiřice inheritance, and thus also the Náchod estate, was acquired by his sister Markéta Salomena. The so-called Winter King Frederick V of the Palatinate, also spent his last night in Bohemia at the local castle, where he stayed overnight during his escape from the country after his defeat at the Battle of White Mountain. Markéta Salomena also left Bohemia shortly thereafter. Among the 27 Czech leaders executed in Old Town Square on June 21, 1621, was Tobiáš Štefek of Koloděje, a citizen of Náchod, member of the Estates Directorate, and regent of the Smiřický estate.

In 1623, Magdalena of the Trčka of Lípa family purchased the Náchod estate and a few years later transferred it to her son Adam Erdman Trčka. Adam was the last owner of the castle to come from the Czech nobility. His brother-in-law was Albrecht von Wallenstein, commander of the imperial army, whose mother also came from the Smiřický family and who was probably born at Náchod Castle in 1583. Adam loyally stood by his relative until his death on February 25, 1634, when he was murdered with him in Cheb.